A tutorial step by step to run a classic Molecular Dynamics Simulation of a protein using GROMACS and building the ions box with PACKMOL.
GROMACS: https://www.gromacs.org/
GROMACS TUTORIALS: http://www.mdtutorials.com/gmx/
PACKMOL: http://leandro.iqm.unicamp.br/m3g/packmol/home.shtml
m3ggroup: https://github.com/m3g